Louis/Rui chooses to be a Jack-of-All-Stats because a leader must be able to adapt and react to any situation. He chose a more balanced and versatile skill set so he'll be ready for anything.
Oliver Collins is a very strong Crutch Character who can kill most early enemies in one or two hits. Is it any wonder he becomes a boss after succumbing to bloodlust and turning into a Lost?
Bayonets using ichor instead of regular bullets: Not only would ammunition be difficult to produce in large quantities in the devastated world, they probably wouldn't be powerful enough to do any real damage to creatures like the Lost. Ichor on the other hand can be turned into powerful munitions thanks to the Revenant's powers, is plentiful and renewable, can be gained by battling enemies, and would not weigh them down like regular ammo. Making it a perfect alternative.
Assuming that the Protagonist has the power to choose whether or not they'll absorb a blood code, it could be that they decided to reject it. Since they didn't want any trace of that monster to live on, especially within themselves.
Alternatively, he doesn't drop one because he explodes rather than turning to ash after being defeated, which most likely destroyed his heart and perma-killed him, leaving no Vestige behind. After all, the Protagonist certainly doesn't mind taking his sword and using it, so why would they feel differently about using his blood code?
Your checkpoints are mistles. Mistletoe is a parasitic plant that attaches to trees and sucks nutrition out of them. In other words, it's a vampire plant.
Each Bloodcode is a reflection of the owner in some way or another.
Riki's code, Assassin, is a Glass Cannon that specializes in sneak attacks and offers large buffs to offense as long as you avoid being hit. Representing how Riki would fight when it suited him and do it well, but was always ready to cut his losses and run when things looked bad.
Yakumo's code, Atlas, focuses on close combat with tremendous physical strength and endurance. The titan Atlas was known for holding the world on his shoulders, and Yakumo is willing to put himself in harm's way and endure enormous struggles to protect his friends.
What did Prometheus steal from the gods to give to humanity? Fire. Louis makes extensive use of blood, and he pursues the secrets of the bloodsprings to provide it to all revenants.
Karen's blood code is Demeter, the goddess of harvest. As the Successor of the Heart, she produces the blood springs and thirst quenching bloodbeads which allow the Revenants to survive.
Jack's code is named after Heimdall, the all-seeing guardian of the Bifrost Bridge. As the watcher and successor of the eye, Jack keeps vigil over the other successors, and can see how close they are to frenzy.
Hades is the god of the underworld, and despite his dubious reputation, was not as bad as he's been made out to be. Silva is a Well-Intentioned Extremist whose done quite a few questionable things, but ultimately has humanities' best interests at heart. Silva also created the Goal of the Mists to keep the Lost and the Revenants contained so neither would threaten the outside world, similar to how Hades kept the dead locked away in the underworld.
Isis was the Egyptian goddess of magic, and Aurora's code specializes in offensive dark gifts. Isis was also the wife of Osiris, and went to great length to find her husband after he was killed and dismembered by his brother Set. Aurora became a successor and placed her crypt above Karen's in order to protect her.
Rin's code is Hephaestus, the forge god who was cast out for having a physical flaw. Rin was scared by her experiences during the war and gave up fighting in favor of becoming a merchant and weapons smith.
Io and Karen:
Io's appearance is startlinglysimilar to Karen, Louis' sister. Beyond the obvious color changes and looking more disheveled and Stripperific, there's arguably a very justified reason for this that the game never touches on: as the Attendants are all Artificial Human clones made by Cruz specifically to care for the Successors, it's entirely plausible that Cruz modeled all of them after Karen, who specifically was her caretaker during Project Q.U.E.E.N.
This also gets reflected elsewhere such as the "Dwellers in the Dark" ending, where Io becomes a tree that helps protect Vein in an identical fashion to Karen becoming the Source of the Blood Beads keeping at least some of the Revenants sane and stable. Or the fact that Karen's attire as a Successor invokes a very similar woman-in-white role to Io.
The Cathedral of The Sacred Blood is a giant labyrinth which has earned a spot as That One Level on the YMMV page. The Successor of the Ribcage, Aurora Valentino, may have done this on purpose in order to help protect Karen, who dwells beneath her crypt and is the source of the Blood Beads helping to sustain the Revenants. Casual looters would take one look at it and turn around, and only the most determined Revenants would even get halfway through the maze... and if they somehow got to the end without turning into Lost, they would likely be running on fumes and be easy prey for Aurora's Attendant.
Why does the protagonist wake on a ruined city road instead of at the bottom of the chasm they fell into after their fight with the Queen? Io probably found them unconscious down there after they reformed, and moved them somewhere they would be safe until they regained consciousness.
Karen, the successor of the Heart is hidden deep inside the Cathedral, protected by the successor of the Ribcage. Kinda like how the ribcage protects vital organs.
Jack Rutherford mentions that a Successor should shape their crypt into something that puts them at ease. Aurora, the successor of the Ribcage, chose to be entombed close to someone she loved.
The game mentions in background lore that the Gen One revenants were deployed against and successfully drove out or killed all the "Horrors" in the city and surrounding area. It's why we never encounter any Aragami in the game, they'd been driven back by the time the Goal of Mists trapped everything inside. There's no telling if this means Revenants are some form of God Eater or if their own abilities are just effective due to their nature, but they apparently work regardless.
Juzo Mido experiments on Revenants and the Lost. What status aliment does he inflict? Inhibit. Which shuts down the powers of both, making all the harder for them to fight back.
The Reveal towards the end of the game that beyond the Gaol of the Mist lies Aragami flips the entire plot on its head. Not only are Aragami canonically a nigh-unstoppable existence of Extreme Omnivore that can automatically devour whatever they come into contact with, but they can evolve based on that. The Revenants we see victimized turn to dead ash like any other, but if one were to able to genuinely consume a Revenant in whole, god only knows what might result.
Given the vampiric nature of the Revenants, even if they somehow bonded with a God Arc or were able to fight an Aragami to a victory, what happens if a Revenant consumed Oracle Cells? Possibly something far, far more dangerous than even what was seen in the game perhaps.
Imagine how dangerous the Protagonist would be if they ever became a Lost. Not only would they be insanely powerful, but also able to absorb the blood code of any Revenants they killed to become even stronger.